After the Japanese attack on Pearl Harbor, the 27th Division deployed to Hawaii. There, Marcus organized and commanded a Ranger Combat Training School, to provide troop training in techniques of unarmed defense to combat Japanese infiltration tactics.[4] But instead of a field command, Marcus was sent to Washington in 1943. He was assigned to the Civil Affairs Division, as chief of planning for occupation governments in territories liberated from the Axis. He accompanied U.S. delegations to the conferences at Cairo, Teheran, Yalta, and Potsdam, and helped draw up the 1943 surrender terms for Italy.[3]

In May 1944, Marcus got himself sent to Britain on Civil Affairs business. He then traded on being a West Point classmate of General Maxwell Taylor to parachute into Normandy on D-Day with the first wave of Taylor's 101st Airborne Division, despite having no paratrooper training.[5] He took informal command of some of the scattered paratroopers and was in combat for a week. After a week in France, he was sent back to the U.S.[3]

After V-E Day in 1945, General Lucius D. Clay asked for Marcus to serve on his staff in the occupation of Germany. Marcus was in charge of providing for the millions of displaced persons in Germany. Clay required all his subordinates to tour the Dachau concentration camp. Marcus was shocked by its horrors; though not previously a Zionist, he began to think differently about a Jewish state.[3]

In 1946, he was named chief of the Army's War Crimes Division in Washington, planning legal and security procedures for the Nuremberg trials and the Tokyo War Crimes Tribunal. He attended the Nuremberg trials, making sure that Nazi crimes were thoroughly documented. After the trials, he was offered promotion to Brigadier General, but instead elected to return to civilian life and his law practice.[3]

US Col. Mickey Marcus in 1948, the first modern Israeli general (Aluf).

In 1947, David Ben-Gurion asked Marcus to recruit an American officer to serve as military advisor to the nascent Jewish army, the Haganah. He could not recruit anyone suitable, so Marcus volunteered himself. In 1948, the U.S. War Department informally acquiesced to Marcus' undertaking, provided he disguised his name and rank to avoid problems with the British authorities in Mandatory Palestine.[citation needed]

He designed a command and control structure for the Haganah, adapting his U.S. Army experience to its special needs. He identified Israel's weakest points in the Negev south, and the Jerusalem area.

Marcus was appointed Aluf ("general") and given command of the Jerusalem front on May 28, 1948. As no ranks were granted to Israeli high command at that time, he became the first general in the fledgling nation's army (see Israel Defense Forces). (Aluf was then equivalent to Brigadier General. Since 1967, Aluf is equivalent to major general.)[6]

He participated in planning Operation Bin Nun Bet and Operation Yoram against the Latrun fort held by the Arab Legion, which blocked the road from Tel Aviv to Jerusalem, which was under siege.[7] Both attacks failed, but Marcus then built the "Burma Road to Jerusalem" - a makeshift winding road through difficult hill terrain, nicknamed after the World War II supply route to China. The "Burma Road" was opened to vehicles on June 10, breaking the siege of Jerusalem, a day before a United Nations cease fire took effect on June 11.

A few hours before the cease fire, Marcus returned to his Central Front headquarters. He and his commanders were billeted in the monks' quarters of the abandoned Monastere Notre Dame de la Nouvelle Alliance in Abu Ghosh.[8] Shortly before 4:00 a.m., a sentry, Eliezer Linski, eighteen years old, and a one-year Palmach veteran, challenged Marcus, who he saw as a figure in white. When Marcus failed to respond with the password, Linski fired in the air and the man ran towards the monastery. He fired at the man, as did one or more fighters in a nearby sentry post. Marcus was found dead, wrapped in a white blanket. As an American Jew, Marcus knew very little Hebrew and failed to understand the Hebrew challenge, and Linski did not understand Marcus who responded in English.[9] Marcus wore no rank, although officers had been recognized by a ribbon pinned to their uniforms. As Marcus's body was removed from Abu Ghosh, a ribbon was found and placed on his casket.

His body was returned to the United States for burial, accompanied by Moshe Dayan and his wife Ruth, Yoseph Harel, and the wife of his aide de camp, Alex Broida.[10]

Ben-Gurion was suspicious of the initial report that Marcus had been shot accidentally.[11] The Haganah was composed of several factions whose lack of consensus over strategy and tactics was one of the reasons for Marcus's appointment as commander for Jerusalem, and Ben-Gurion suspected that elements in the Palmach may have conspired to kill Marcus so he would be replaced. On the same day Marcus was shot, Ben-Gurion summoned Yaakov Shimshon Shapira—later Israel's Attorney General—and asked him to investigate the incident. Shapira's investigation was cursory. Despite conflicting reports concerning the number of shots fired, how many wounds Marcus suffered, whether the fatal wound could have been caused by Linski's rifle, and how and why Marcus may have been outside the monastery, he concluded that Linski shot Marcus in the line of duty. The report has never been made public.[12]

Marcus' grave is the only one in the West Point Cemetery at the United States Military Academy for an American killed fighting under the flag of another country; he was still eligible for interment there because he was a graduate of the academy who served honorably. His gravestone at West Point reads: "Colonel David Marcus—a Soldier for All Humanity". A memorial plaque in his honor is located in the lobby of the Union Temple of Brooklyn where his funeral service was conducted. It reads "Killed in action in the hills of Zion while leading Israeli forces as their supreme commander in the struggle for Israel's freedom—Blessed is the match that is consumed in kindling flame/ Blessed is the flame that burns in the secret fastness of the heart/ Blessed is the heart with strength to stop its beating for honor's sake/ Blessed is the match that is consumed in kindling flame—Dedicated by his fellow members of Union Temple of Brooklyn December 9, 1949." Ben-Gurion wrote to Marcus's wife Emma in Brooklyn, New York: "Marcus was the best man we had".[13] On May 10, 1951, Ben-Gurion laid a wreath at the Marcus grave, accompanied by Emma Marcus.[14] In January 2015 Israel's President, Reuven Rivlin, visited the United States Military Academy at West Point and spoke at Marcus' grave: "For me, he was the first general of the IDF in every sense of the word. He had a sense of purpose and mission, in the establishment of the Israel Defense Forces, he taught us how to act as an army in our early days, and was one of Ben-Gurion’s greatest military advisors. There is no one who better illustrates the strong bond between Israel and the United States."[15]